cctbx.euclidean_model_matching
index
/net/chevy/raid1/nat/src/cctbx_project/cctbx/euclidean_model_matching.py

 
Modules
       
boost
cctbx.crystal
scitbx.python_utils.dicts
cctbx_emma_ext
cctbx.array_family.flex
math
scitbx.matrix
cctbx.sgtbx
sys

 
Classes
       
__builtin__.object
delegating_model_matches
model_matches
euclidean_match_symmetry
match_refine
position
cctbx.crystal.special_position_settings(cctbx.crystal.symmetry)
model

 
class delegating_model_matches(__builtin__.object)
    emma loops over all pairs of sites from the first and second structure.
If a pair is closer than tolerance (under Euclidean symmetry) it
initiates a "match and refine" procedure which incrementally adds the
"next closest" pair, with a distance below 2*tolerance. Each time
a pair is added the allowed origin shifts (if any) are refined to
minimize the rmsd of all the pairs matched so far. When there are
no more pairs to add, emma goes into a "weeding" procedure. This
procedure sorts the pairs by distance. If there are distances above
tolerance, the worst pair is removed, followed by the same allowed
origin shift refinement as before. The weeding is repeated until
there are no pairs above tolerance.
 
emma was written with substructures in mind, which usually have a few
(by macromolecular standards) sites placed far apart in space.
 
  Methods defined here:
__init__(self, model1, model2, tolerance=1.0, models_are_diffraction_index_equivalent=False, shall_break=None, rms_penalty_per_site=0.05)
consensus_model(self, i_model=1, i_refined_matches=0)
n_matches(self)
n_pairs_best_match(self)
transform_model(self, i_model, i_refined_matches=0)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class euclidean_match_symmetry(__builtin__.object)
     Methods defined here:
__init__(self, space_group_info, use_k2l, use_l2n)
filter_shift(self, shift, selector=1)
show(self, title='', f=None)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class match_refine(__builtin__.object)
     Methods defined here:
__init__(self, tolerance, ref_model1, ref_model2, match_symmetry, add_pair_ext, i_pivot1, i_pivot2, eucl_symop, initial_shift, times=None)
add_pairs(self)
apply_eucl_ops(self, i_model2)
calculate_rms(self)
calculate_shortest_diff(self, pair)
calculate_shortest_diffs(self)
calculate_shortest_dist(self, pair)
eliminate_weak_pairs(self)
exclude_pairs(self)
get_transformed_model2(self, output_pdb=None, scattering_type='SE', f=<open file '<stdout>', mode 'w'>, return_superposed_model2=True)
refine_adjusted_shift(self)
show(self, f=None, truncate_singles=None, singles_per_line=5)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class model(cctbx.crystal.special_position_settings)
    
Method resolution order:
model
cctbx.crystal.special_position_settings
cctbx.crystal.symmetry
__builtin__.object

Methods defined here:
__getitem__(self, key)
__init__(self, special_position_settings, positions=None)
__len__(self)
add_position(self, pos)
add_positions(self, positions)
as_xray_structure(self, scatterer=None)
best_superpositions_on_other(self, other_model, tolerance=1.5, models_are_diffraction_index_equivalent=True, break_if_match_with_no_singles=True, f=<open file '<stdout>', mode 'w'>, specifically_test_inverse=True)
cb_op(self)
change_basis(self, cb_op)
change_hand(self)
combine_with_other(self, other_model, tolerance=1.5, models_are_diffraction_index_equivalent=True, break_if_match_with_no_singles=True, f=<open file '<stdout>', mode 'w'>, improved_only=True, new_model_number=0)
expand_to_p1(self)
positions(self)
reset_cb_op(self)
show(self, title, f=None)
size(self)
transform_to_reference_setting(self)

Methods inherited from cctbx.crystal.special_position_settings:
assert_min_distance_sym_equiv(self)
asu_mappings(self, buffer_thickness, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_is_inside_epsilon=None)
incremental_pairs(self, distance_cutoff, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1)
min_distance_sym_equiv(self)
pair_asu_table(self, distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, min_cubicle_edge=5, distance_cutoff_epsilon=None)
pair_generator(self, distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, minimal=False)
site_cluster_analysis(self, min_distance=None, min_cross_distance=None, min_self_distance=None, general_positions_only=False, estimated_reduction_factor=4, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, min_cubicle_edge=5, cubicle_epsilon=-1)
site_symmetry(self, site=None, site_cart=None)
site_symmetry_table(self, sites_frac=None, sites_cart=None, unconditional_general_position_flags=None)
sym_equiv_sites(self, site)
u_star_tolerance(self)
xray_structure(self, scatterers=None)

Methods inherited from cctbx.crystal.symmetry:
as_cif_block(self)
as_py_code(self, indent='')
as_reference_setting(self)
average_b_cart(self, b_cart)
average_u_cart(self, u_cart)
best_cell(self, angular_tolerance=None)
build_miller_set(self, anomalous_flag, d_min, d_max=None)
cell_equivalent_p1(self)
change_of_basis_op_to_best_cell(self, angular_tolerance=None, best_monoclinic_beta=True)
change_of_basis_op_to_inverse_hand(self)
change_of_basis_op_to_minimum_cell(self)
change_of_basis_op_to_niggli_cell(self, relative_epsilon=None, iteration_limit=None)
change_of_basis_op_to_primitive_setting(self)
change_of_basis_op_to_reference_setting(self)
customized_copy(self, unit_cell=<class libtbx.utils.Keep>, space_group_info=<class libtbx.utils.Keep>, raise_sorry_if_incompatible_unit_cell=False)
direct_space_asu(self)
gridding(self, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
inverse_hand(self)
is_compatible_unit_cell(self)
is_patterson_symmetry(self)
is_similar_symmetry(self, other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0)
join_symmetry(self, other_symmetry, force=False, raise_sorry_if_incompatible_unit_cell=False)
miller_set(self, indices, anomalous_flag)
minimum_cell(self)
niggli_cell(self, relative_epsilon=None, iteration_limit=None)
patterson_symmetry(self)
primitive_setting(self)
reflection_intensity_symmetry(self, anomalous_flag)
show_summary(self, f=None, prefix='')
space_group(self)
space_group_info(self)
special_position_settings(self, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)
subtract_continuous_allowed_origin_shifts(self, translation_cart)
unit_cell(self)

Data descriptors inherited from cctbx.crystal.symmetry:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class model_matches(delegating_model_matches)
    
Method resolution order:
model_matches
delegating_model_matches
__builtin__.object

Methods defined here:
__init__(self, model1, model2, tolerance=1.0, models_are_diffraction_index_equivalent=False, break_if_match_with_no_singles=False, rms_penalty_per_site=0.05)

Methods inherited from delegating_model_matches:
consensus_model(self, i_model=1, i_refined_matches=0)
n_matches(self)
n_pairs_best_match(self)
transform_model(self, i_model, i_refined_matches=0)

Data descriptors inherited from delegating_model_matches:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class position(__builtin__.object)
     Methods defined here:
__init__(self, label, site)
__repr__(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
compute_refined_matches(ref_model1, ref_model2, tolerance, models_are_diffraction_index_equivalent, shall_break)
filter_shift(continuous_shift_flags, shift, selector=1)
generate_singles(n, i)
match_refine_times()
match_rt_from_ref_eucl_rt(model1_cb_op, model2_cb_op, ref_eucl_rt)
match_sort_function(match_a, match_b)
pair_sort_function(pair_a, pair_b)
sgtbx_rt_mx_as_matrix_rt(s)
weed_refined_matches(space_group_number, refined_matches, rms_penalty_per_site)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)